Recombinant LSDV Strains in Asia: Vaccine Spillover or Natural Emergence?
Abstract
:1. Introduction
2. Materials and Methods
2.1. Comparison of Published Recombinant LSDV Genomes
2.2. Vaccine Batches
2.3. DNA Purification
2.4. Pre-Sequencing Enrichment
2.5. Library Preparation and Sequencing
2.6. Sequencing Data Processing
2.7. De Novo Assembly without In Silico Enrichment
2.8. De Novo Assembly with In Silico Enrichment
3. Results
3.1. Data Output of the Different Sequencing Libraries
3.2. Composition of the Lumpivax Vaccine
3.3. Reconstruction of the CaPV Strains Present in the Lumpivax Vaccine
3.3.1. Reconstruction of the Lumpivax GTPV Strain
3.3.2. Reconstruction of the Lumpivax LSDV Vaccine Strains
3.4. Presence of the Vaccine-like Recombinant LSDV Strains
3.4.1. Recombination Patterns of the Recombinant Field LSDV Strains
3.4.2. Reconstruction of the Vaccine-like Recombinant LSDV Strains
3.4.3. Recombination Breakpoint Analysis
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- Walker, P.J.; Siddell, S.G.; Lefkowitz, E.J.; Mushegian, A.R.; Dempsey, D.M.; Dutilh, B.E.; Harrach, B.; Harrison, R.L.; Hendrickson, R.C.; Junglen, S.; et al. Changes to Virus Taxonomy and the International Code of Virus Classification and Nomenclature Ratified by the International Committee on Taxonomy of Viruses (2019). Arch. Virol. 2019, 164, 2417–2429. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Tulman, E.R.; Afonso, C.L.; Lu, Z.; Zsak, L.; Kutish, G.F.; Rock, D.L. Genome of Lumpy Skin Disease Virus. J. Virol. 2001, 75, 7122–7130. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Tulman, E.R.; Afonso, C.L.; Lu, Z.; Zsak, L.; Sur, J.H.; Sandybaev, N.T.; Kerembekova, U.Z.; Zaitsev, V.L.; Kutish, G.F.; Rock, D.L. The Genomes of Sheeppox and Goatpox Viruses. J. Virol. 2002, 76, 6054–6061. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Le Goff, C.; Lamien, C.E.; Fakhfakh, E.; Chadeyras, A.; Aba-Adulugba, E.; Libeau, G.; Tuppurainen, E.; Wallace, D.B.; Adam, T.; Silber, R.; et al. Capripoxvirus G-Protein-Coupled Chemokine Receptor: A Host-Range Gene Suitable for Virus Animal Origin Discrimination. J. Gen. Virol. 2009, 90, 1967–1977. [Google Scholar] [CrossRef] [PubMed]
- Lamien, C.E.; Le Goff, C.; Silber, R.; Wallace, D.B.; Gulyaz, V.; Tuppurainen, E.; Madani, H.; Caufour, P.; Adam, T.; El Harrak, M.; et al. Use of the Capripoxvirus Homologue of Vaccinia Virus 30 KDa RNA Polymerase Subunit (RPO30) Gene as a Novel Diagnostic and Genotyping Target: Development of a Classical PCR Method to Differentiate Goat Poxvirus from Sheep Poxvirus. Vet. Microbiol. 2011, 149, 30–39. [Google Scholar] [CrossRef] [PubMed]
- Mathijs, E.; Vandenbussche, F.; Van Borm, S. Using Genomics for Surveillance of Veterinary Infectious Agents. Rev. Sci. Tech. Int. Off. Epizoot. 2016, 35, 143–157. [Google Scholar] [CrossRef]
- Cottam, E.M.; Wadsworth, J.; Shaw, A.E.; Rowlands, R.J.; Goatley, L.; Maan, S.; Maan, N.S.; Mertens, P.P.C.; Ebert, K.; Li, Y.; et al. Transmission Pathways of Foot-and-Mouth Disease Virus in the United Kingdom in 2007. PLoS Pathog. 2008, 4, e1000050. [Google Scholar] [CrossRef] [Green Version]
- World Organisation for Animal Health (OIE). Terrestrial Animal Health Code (2021). Chapter 1.3: Diseases, Infections and Infestations Listed by the OIE. Available online: https://www.woah.org/fileadmin/Home/eng/Health_standards/tahc/current/chapitre_oie_listed_disease.pdf (accessed on 17 February 2022).
- Tuppurainen, E.S.; Venter, E.H.; Shisler, J.L.; Gari, G.; Mekonnen, G.A.; Juleff, N.; Lyons, N.A.; Clercq, K.D.; Upton, C.; Bowden, T.R.; et al. Review: Capripoxvirus Diseases: Current Status and Opportunities for Control. Transbound. Emerg. Dis. 2017, 64, 729–745. [Google Scholar] [CrossRef]
- Tuppurainen, E.; Dietze, K.; Wolff, J.; Bergmann, H.; Beltran-Alcrudo, D.; Fahrion, A.; Lamien, C.E.; Busch, F.; Sauter-Louis, C.; Conraths, F.J.; et al. Review: Vaccines and Vaccination against Lumpy Skin Disease. Vaccines 2021, 9, 1136. [Google Scholar] [CrossRef]
- Kitching, R.P. Vaccines for Lumpy Skin Disease, Sheep Pox and Goat Pox. Dev. Biol. 2003, 114, 161–167. [Google Scholar]
- Babiuk, S. Vaccines against LSD and Vaccination Strategies. In Lumpy Skin Disease; Tuppurainen, E.S.M., Babiuk, S., Klement, E., Eds.; Springer International Publishing: Cham, Switzerland, 2018; pp. 85–93. ISBN 978-3-319-92411-3. [Google Scholar]
- Klement, E.; Broglia, A.; Antoniou, S.E.; Tsiamadis, V.; Plevraki, E.; Petrovic, T.; Polacek, V.; Debeljak, Z.; Miteva, A.; Alexandrov, T.; et al. Neethling Vaccine Proved Highly Effective in Controlling Lumpy Skin Disease Epidemics in the Balkans. Prev. Vet. Med. 2018, 181, 104595. [Google Scholar] [CrossRef] [PubMed]
- Morgenstern, M.; Klement, E. The Effect of Vaccination with Live Attenuated Neethling Lumpy Skin Disease Vaccine on Milk Production and Mortality—An Analysis of 77 Dairy Farms in Israel. Vaccines 2020, 8, 324. [Google Scholar] [CrossRef]
- Bamouh, Z.; Hamdi, J.; Fellahi, S.; Khayi, S.; Jazouli, M.; Tadlaoui, K.O.; Fihri, O.F.; Tuppurainen, E.; Elharrak, M. Investigation of Post Vaccination Reactions of Two Live Attenuated Vaccines against Lumpy Skin Disease of Cattle. Vaccines 2021, 9, 621. [Google Scholar] [CrossRef] [PubMed]
- Haegeman, A.; De Leeuw, I.; Mostin, L.; Campe, W.V.; Aerts, L.; Venter, E.; Tuppurainen, E.; Saegerman, C.; De Clercq, K. Comparative Evaluation of Lumpy Skin Disease Virus-Based Live Attenuated Vaccines. Vaccines 2021, 9, 473. [Google Scholar] [CrossRef] [PubMed]
- Tuppurainen, E.S.; Pearson, C.R.; Bachanek-Bankowska, K.; Knowles, N.J.; Amareen, S.; Frost, L.; Henstock, M.R.; Lamien, C.E.; Diallo, A.; Mertens, P.P. Characterization of Sheep Pox Virus Vaccine for Cattle against Lumpy Skin Disease Virus. Antivir. Res. 2014, 109, 1–6. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Vandenbussche, F.; Mathijs, E.; Haegeman, A.; Al-Majali, A.; Van Borm, S.; De Clercq, K. Complete Genome Sequence of Capripoxvirus Strain KSGP 0240 from a Commercial Live Attenuated Vaccine. Genome Announc. 2016, 4, e01114-16. [Google Scholar] [CrossRef] [Green Version]
- Gari, G.; Abie, G.; Gizaw, D.; Wubete, A.; Kidane, M.; Asgedom, H.; Bayissa, B.; Ayelet, G.; Oura, C.A.; Roger, F.; et al. Evaluation of the Safety, Immunogenicity and Efficacy of Three Capripoxvirus Vaccine Strains against Lumpy Skin Disease Virus. Vaccine 2015, 33, 3256–3261. [Google Scholar] [CrossRef]
- Zhugunissov, K.; Bulatov, Y.; Orynbayev, M.; Kutumbetov, L.; Abduraimov, Y.; Shayakhmetov, Y.; Taranov, D.; Amanova, Z.; Mambetaliyev, M.; Absatova, Z.; et al. Goatpox Virus (G20-LKV) Vaccine Strain Elicits a Protective Response in Cattle against Lumpy Skin Disease at Challenge with Lumpy Skin Disease Virulent Field Strain in a Comparative Study. Vet. Microbiol. 2020, 245, 108695. [Google Scholar] [CrossRef]
- Ayelet, G.; Abate, Y.; Sisay, T.; Nigussie, H.; Gelaye, E.; Jemberie, S.; Asmare, K. Lumpy Skin Disease: Preliminary Vaccine Efficacy Assessment and Overview on Outbreak Impact in Dairy Cattle at Debre Zeit, Central Ethiopia. Antivir. Res. 2013, 98, 261–265. [Google Scholar] [CrossRef]
- Brenner, J.; Bellaiche, M.; Gross, E.; Elad, D.; Oved, Z.; Haimovitz, M.; Wasserman, A.; Friedgut, O.; Stram, Y.; Bumbarov, V.; et al. Appearance of Skin Lesions in Cattle Populations Vaccinated against Lumpy Skin Disease: Statutory Challenge. Vaccine 2009, 27, 1500–1503. [Google Scholar] [CrossRef]
- Ben-Gera, J.; Klement, E.; Khinich, E.; Stram, Y.; Shpigel, N.Y. Comparison of the Efficacy of Neethling Lumpy Skin Disease Virus and X10RM65 Sheep-Pox Live Attenuated Vaccines for the Prevention of Lumpy Skin Disease—The Results of a Randomized Controlled Field Study. Vaccine 2015, 33, 4837–4842. [Google Scholar] [CrossRef] [PubMed]
- Sevik, M.; Dogan, M. Epidemiological and Molecular Studies on Lumpy Skin Disease Outbreaks in Turkey during 2014–2015. Transbound. Emerg. Dis. 2017, 64, 1268–1279. [Google Scholar] [CrossRef] [PubMed]
- Hamdi, J.; Bamouh, Z.; Jazouli, M.; Boumart, Z.; Tadlaoui, K.O.; Fihri, O.F.; EL Harrak, M. Experimental Evaluation of the Cross-Protection between Sheeppox and Bovine Lumpy Skin Vaccines. Sci. Rep. 2020, 10, 8888. [Google Scholar] [CrossRef] [PubMed]
- Sprygin, A.; Babin, Y.; Pestova, Y.; Kononova, S.; Wallace, D.B.; Van Schalkwyk, A.; Byadovskaya, O.; Diev, V.; Lozovoy, D.; Kononov, A. Analysis and Insights into Recombination Signals in Lumpy Skin Disease Virus Recovered in the Field. PLoS ONE 2018, 13, e0207480. [Google Scholar] [CrossRef]
- Kononov, A.; Byadovskaya, O.; Kononova, S.; Yashin, R.; Zinyakov, N.; Mischenko, V.; Perevozchikova, N.; Sprygin, A. Detection of Vaccine-like Strains of Lumpy Skin Disease Virus in Outbreaks in Russia in 2017. Arch. Virol. 2019, 164, 1575–1585. [Google Scholar] [CrossRef]
- Agianniotaki, E.I.; Mathijs, E.; Vandenbussche, F.; Tasioudi, K.E.; Haegeman, A.; Iliadou, P.; Chaintoutis, S.C.; Dovas, C.I.; Van Borm, S.; Chondrokouki, E.D.; et al. Complete Genome Sequence of the Lumpy Skin Disease Virus Isolated from the First Reported Case in Greece in 2015. Genome Announc. 2017, 5, e00550-17. [Google Scholar] [CrossRef] [Green Version]
- Mathijs, E.; Vandenbussche, F.; Saduakassova, M.; Kabduldanov, T.; Haegeman, A.; Aerts, L.; Kyzaibayev, T.; Sultanov, A.; Van Borm, S.; De Clercq, K. Complete Coding Sequence of a Lumpy Skin Disease Virus Strain Isolated during the 2016 Outbreak in Kazakhstan. Microbiol. Resour. Announc. 2020, 9, e01399-19. [Google Scholar] [CrossRef] [Green Version]
- Mathijs, E.; Vandenbussche, F.; Ivanova, E.; Haegeman, A.; Aerts, L.; De Leeuw, I.; Van Borm, S.; De Clercq, K. Complete Coding Sequence of a Lumpy Skin Disease Virus from an Outbreak in Bulgaria in 2016. Microbiol. Resour. Announc. 2020, 9, e00977-20. [Google Scholar] [CrossRef]
- Sprygin, A.; Babin, Y.; Pestova, Y.; Kononova, S.; Byadovskaya, O.; Kononov, A. Complete Genome Sequence of the Lumpy Skin Disease Virus Recovered from the First Outbreak in the Northern Caucasus Region of Russia in 2015. Microbiol. Resour. Announc. 2019, 8, e01733-18. [Google Scholar] [CrossRef] [Green Version]
- Flannery, J.; Shih, B.; Haga, I.R.; Ashby, M.; Corla, A.; King, S.; Freimanis, G.; Polo, N.; Tse, A.C.; Brackman, C.J.; et al. A Novel Strain of Lumpy Skin Disease Virus Causes Clinical Disease in Cattle in Hong Kong. Transbound. Emerg. Dis. 2021. [Google Scholar] [CrossRef]
- Ma, J.; Yuan, Y.; Shao, J.; Sun, M.; He, W.; Chen, J.; Liu, Q. Genomic Characterization of Lumpy Skin Disease Virus in Southern China. Transbound. Emerg. Dis. 2021. [Google Scholar] [CrossRef] [PubMed]
- Mathijs, E.; Vandenbussche, F.; Nguyen, L.; Aerts, L.; Nguyen, T.; De Leeuw, I.; Quang, M.; Nguyen, H.D.; Philips, W.; Dam, T.V.; et al. Coding-Complete Sequences of Recombinant Lumpy Skin Disease Viruses Collected in 2020 from Four Outbreaks in Northern Vietnam. Microbiol. Resour. Announc. 2021, 10, e0089721. [Google Scholar] [CrossRef] [PubMed]
- Huang, C.-W.; Ting, L.-J.; Liu, Y.-P.; Lin, Y.-J.; Lee, F.; Chiou, C.-J. Complete Coding Sequence of Lumpy Skin Disease Virus Isolated from Kinmen Island, Taiwan, in 2020. Microbiol. Resour. Announc. 2022, 11, e0120421. [Google Scholar] [CrossRef] [PubMed]
- Orynbayev, M.B.; Nissanova, R.K.; Khairullin, B.M.; Issimov, A.; Zakarya, K.D.; Sultankulova, K.T.; Kutumbetov, L.B.; Tulendibayev, A.B.; Myrzakhmetova, B.S.; Burashev, E.D.; et al. Lumpy Skin Disease in Kazakhstan. Trop. Anim. Health Prod. 2021, 53, 166. [Google Scholar] [CrossRef]
- Sprygin, A.; Pestova, Y.; Prutnikov, P.; Kononov, A. Detection of Vaccine-like Lumpy Skin Disease Virus in Cattle and Musca Domestica, L. Flies in an Outbreak of Lumpy Skin Disease in Russia in 2017. Transbound. Emerg. Dis. 2018, 65, 1137–1144. [Google Scholar] [CrossRef]
- Tuppurainen, E.S.M.; Antoniou, S.-E.; Tsiamadis, E.; Topkaridou, M.; Labus, T.; Debeljak, Z.; Plavšić, B.; Miteva, A.; Alexandrov, T.; Pite, L.; et al. Field Observations and Experiences Gained from the Implementation of Control Measures against Lumpy Skin Disease in South-East Europe between 2015 and 2017. Prev. Vet. Med. 2020, 181, 104600. [Google Scholar] [CrossRef]
- European Food Safety Authority (EFSA); Calistri, P.; De Clercq, K.; Gubbins, S.; Klement, E.; Stegeman, A.; Cortiñas Abrahantes, J.; Marojevic, D.; Antoniou, S.-E.; Broglia, A. Lumpy Skin Disease Epidemiological Report IV: Data Collection and Analysis. EFSA J. 2020, 18, e06010. [Google Scholar] [CrossRef] [Green Version]
- Haegeman, A.; De Leeuw, I.; Saduakassova, M.; Van Campe, W.; Aerts, L.; Philips, W.; Sultanov, A.; Mostin, L.; De Clercq, K. The Importance of Quality Control of LSDV Live Attenuated Vaccines for Its Safe Application in the Field. Vaccines 2021, 9, 1019. [Google Scholar] [CrossRef]
- Katoh, K.; Standley, D.M. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. Mol. Biol. Evol. 2013, 30, 772–780. [Google Scholar] [CrossRef] [Green Version]
- Tu, S.-L.; Staheli, J.P.; McClay, C.; McLeod, K.; Rose, T.M.; Upton, C. Base-By-Base Version 3: New Comparative Tools for Large Virus Genomes. Viruses 2018, 10, 637. [Google Scholar] [CrossRef] [Green Version]
- Mathijs, E.; Haegeman, A.; De Clercq, K.; Van Borm, S.; Vandenbussche, F. A Robust, Cost-Effective and Widely Applicable Whole-Genome Sequencing Protocol for Capripoxviruses. J. Virol. Methods 2022, 301, 114464. [Google Scholar] [CrossRef] [PubMed]
- FastQC: A Quality Control Tool for High Throughput Sequence Data. Available online: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ (accessed on 19 February 2018).
- Bolger, A.M.; Lohse, M.; Usadel, B. Trimmomatic: A Flexible Trimmer for Illumina Sequence Data. Bioinformatics 2014, 30, 2114–2120. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- BBMap Short Read Aligner, and Other Bioinformatic Tools. Available online: https://sourceforge.net/projects/bbmap/ (accessed on 24 September 2021).
- Wickham, H. Ggplot2: Elegant Graphics for Data Analysis; Springer International Publishing: Cham, Switzerland, 2016; ISBN 978-3-319-24277-4. [Google Scholar]
- Bankevich, A.; Nurk, S.; Antipov, D.; Gurevich, A.A.; Dvorkin, M.; Kulikov, A.S.; Lesin, V.M.; Nikolenko, S.I.; Pham, S.; Prjibelski, A.D.; et al. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. J. Comput. Biol. 2012, 19, 455–477. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Mikheenko, A.; Prjibelski, A.; Saveliev, V.; Antipov, D.; Gurevich, A. Versatile Genome Assembly Evaluation with QUAST-LG. Bioinformatics 2018, 34, i142–i150. [Google Scholar] [CrossRef] [PubMed]
- Biswas, S.; Noyce, R.S.; Babiuk, L.A.; Lung, O.; Bulach, D.M.; Bowden, T.R.; Boyle, D.B.; Babiuk, S.; Evans, D.H. Extended Sequencing of Vaccine and Wild-Type Capripoxvirus Isolates Provides Insights into Genes Modulating Virulence and Host Range. Transbound. Emerg. Dis. 2020, 67, 80–97. [Google Scholar] [CrossRef]
- Mathijs, E.; Vandenbussche, F.; Haegeman, A.; King, A.; Nthangeni, B.; Potgieter, C.; Maartens, L.; Van Borm, S.; De Clercq, K. Complete Genome Sequences of the Neethling-Like Lumpy Skin Disease Virus Strains Obtained Directly from Three Commercial Live Attenuated Vaccines. Genome Announc. 2016, 4, e01255-16. [Google Scholar] [CrossRef] [Green Version]
- Amirgazin, A.; Ragatova, A. Lumpy Skin Disease Virus Strain KZ-Kostanay-2018, Partial Genome (GenBank: MT992618.1). Available online: https://www.ncbi.nlm.nih.gov/nuccore/MT992618.1 (accessed on 1 April 2022).
- Lu, G.; Xie, J.; Luo, J.; Shao, R.; Jia, K.; Li, S. Lumpy Skin Disease Outbreaks in China, since August 3, 2019. Transbound. Emerg. Dis. 2020, 68, 216–219. [Google Scholar] [CrossRef]
- Wang, Y.; Zhao, L.; Yang, J.; Shi, M.; Nie, F.; Liu, S.; Wang, Z.; Huang, D.; Wu, H.; Li, D.; et al. Analysis of Vaccine-like Lumpy Skin Disease Virus from Flies near the Western Border of China. Transbound. Emerg. Dis. 2021. [Google Scholar] [CrossRef]
- Tran, H.T.T.; Truong, A.D.; Dang, A.K.; Ly, D.V.; Nguyen, C.T.; Chu, N.T.; Hoang, T.V.; Nguyen, H.T.; Nguyen, V.T.; Dang, H.V. Lumpy Skin Disease Outbreaks in Vietnam, 2020. Transbound. Emerg. Dis. 2021, 68, 977–980. [Google Scholar] [CrossRef]
- Sprygin, A.; Pestova, Y.; Bjadovskaya, O.; Prutnikov, P.; Zinyakov, N.; Kononova, S.; Ruchnova, O.; Lozovoy, D.; Chvala, I.; Kononov, A. Evidence of Recombination of Vaccine Strains of Lumpy Skin Disease Virus with Field Strains, Causing Disease. PLoS ONE 2020, 15, e0232584. [Google Scholar] [CrossRef]
- Sprygin, A.; Van Schalkwyk, A.; Shumilova, I.; Nesterov, A.; Kononova, S.; Prutnikov, P.; Byadovskaya, O.; Kononov, A. Full-Length Genome Characterization of a Novel Recombinant Vaccine-like Lumpy Skin Disease Virus Strain Detected during the Climatic Winter in Russia, 2019. Arch. Virol. 2020, 165, 2675–2677. [Google Scholar] [CrossRef] [PubMed]
- World Organisation for Animal Health (OIE). Manual of Diagnostic Tests and Vaccines for Terrestrial Animals. Chapter 2.3.4: Minimum Requirements for the Production and Quality Control of Vaccines (Version Adopted in May 2018). Available online: https://www.woah.org/fileadmin/Home/eng/Health_standards/tahm/2.03.04_MANU_SITES_VACCINE_PROD_CONTROL.pdf (accessed on 17 February 2022).
- World Organisation for Animal Health (OIE). Manual of Diagnostic Tests and Vaccines for Terrestrial Animals. Chapter 1.1.8: Principles of Veterinary Vaccine Production (Version Adopted in May 2018). Available online: https://www.woah.org/fileadmin/Home/eng/Health_standards/tahm/1.01.08_VACCINE_PRODUCTION.pdf (accessed on 17 February 2022).
- Qin, L.; Upton, C.; Hazes, B.; Evans, D.H. Genomic Analysis of the Vaccinia Virus Strain Variants Found in Dryvax Vaccine. J. Virol. 2011, 85, 13049–13060. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Qin, L.; Evans, D.H. Genome Scale Patterns of Recombination between Coinfecting Vaccinia Viruses. J. Virol. 2014, 88, 5277–5286. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Saltykov, Y.V.; Kolosova, A.A.; Filonova, N.N.; Chichkin, A.N.; Feodorova, V.A. Genetic Evidence of Multiple Introductions of Lumpy Skin Disease Virus into Saratov Region, Russia. Pathogens 2021, 10, 716. [Google Scholar] [CrossRef] [PubMed]
Output Metric | B-0517_DNA | B-0517_PCR | B-0219_PCR |
---|---|---|---|
Paired-end raw reads | 3,526,949 | 3,176,585 | 3,106,361 |
Paired-end reads after quality trimming | 3,512,424 | 3,149,127 | 3,073,447 |
Proportion of reads mapping to NI-2490 1 (%) | 83.29 | 99.66 | 99.50 |
Proportion of NI-2490 1 genome covered (%) | 100.00 | 99.89 | 99.86 |
Quality Metric | B-0517_PCR | B-0219_PCR |
---|---|---|
Genome fraction (%) | 90.169 | 94.091 |
Duplication ratio | 1.058 | 1.092 |
GC (%) | 25.82 | 25.24 |
Contigs | 126 | 45 |
Contigs (≥1000 bp) | 51 | 31 |
Contigs (≥5000 bp) | 1 | 14 |
Contigs (≥10,000 bp) | 0 | 5 |
Mismatches per 100 kbp | 279.32 | 2202.11 |
InDels per 100 kbp | 21.59 | 124.14 |
LGA50 1 | 35 | 7 |
NGA50 2 | 1370 | 6783 |
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Vandenbussche, F.; Mathijs, E.; Philips, W.; Saduakassova, M.; De Leeuw, I.; Sultanov, A.; Haegeman, A.; De Clercq, K. Recombinant LSDV Strains in Asia: Vaccine Spillover or Natural Emergence? Viruses 2022, 14, 1429. https://doi.org/10.3390/v14071429
Vandenbussche F, Mathijs E, Philips W, Saduakassova M, De Leeuw I, Sultanov A, Haegeman A, De Clercq K. Recombinant LSDV Strains in Asia: Vaccine Spillover or Natural Emergence? Viruses. 2022; 14(7):1429. https://doi.org/10.3390/v14071429
Chicago/Turabian StyleVandenbussche, Frank, Elisabeth Mathijs, Wannes Philips, Meruyert Saduakassova, Ilse De Leeuw, Akhmetzhan Sultanov, Andy Haegeman, and Kris De Clercq. 2022. "Recombinant LSDV Strains in Asia: Vaccine Spillover or Natural Emergence?" Viruses 14, no. 7: 1429. https://doi.org/10.3390/v14071429
APA StyleVandenbussche, F., Mathijs, E., Philips, W., Saduakassova, M., De Leeuw, I., Sultanov, A., Haegeman, A., & De Clercq, K. (2022). Recombinant LSDV Strains in Asia: Vaccine Spillover or Natural Emergence? Viruses, 14(7), 1429. https://doi.org/10.3390/v14071429